what is mass spectrometry?
It measures mass-to-charge ratios to identify / quantify biomolecules
what is the process of mass spectrometry
ionizing a sample
separating the ions by their mass-to-charge ratio (m/z)
detecting them to generate a mass spectrum
interactome
The complete set of molecular interactions within a cell or organism, typically focusing on protein-protein interactions
origin of python
Python is named after the British comedy group Monty Python, not the snake. The language's creator, Guido van Rossum, wanted something "short, unique, and slightly mysterious," and he was a fan of Monty Python's Flying Circus
Chaithra Umesh
Dr. Krishna Pal Singh
Kristian Schultz
Clémence Réda
Manjunath Mahendra
Rahul Bordoloi
Alexandra Baumann
Peggy Sterling
Christina Stanke
Ronja Müller
Mahla Haghzad
inflammation
Inflammation is the body's natural response to injury or infection.
It's a protective mechanism where the immune system releases chemicals to protect and repair tissues.
the inflammation process involves…
increased blood flow
immune cell activation
the release of substances that help to remove harmful agents and begin healing
acute inflammation
Acute inflammation is the immediate, short-term response to injury or infection
Ist characterized by redness, heat, swelling, and pain.
chronic inflammation
Chronic inflammation is a longer-term response that can result from persistent infections, autoimmune conditions, or long-term exposure to irritants.
It can lead to tissue damage and is associated with various diseases like arthritis, heart disease, and cancer.
Translator
program to translate source code to machine language
allow us to give the machine instructions
either an interpreter or compiler
Interpreter
translates line by line and executes the line before going to the next line
(python usually uses interpreter)
Compiler
translate the code all at once, read the entire file
then executes all at once
print(type(2))
print(type(2.5))
print(type(‘hi hello there’))
print (type(str(100)))
print (type(int(str(100))))
<class 'int'> integer
<class 'float'> floating point number
<class 'str'> string
print (2 ** 2)
print (2 ** 3)
print (2 ** 4)
4
8
16
(exponential)
print (2 // 4)
print (3 // 4)
print (5 // 4)
0
1
(rounded to an integer)
print (5 % 4)
print (6 % 4)
2
(whats the remaining of the division)
print (round (3.1))
3
print (abs(-20))
20
(no negative numbers)
operator precedence
print (20 - 3 * 4)
different operators have different precedence
was wird statt camelCase in python bei variablen verwendet
snake_case
start with lowercase or underscore
case sensitive
cant overwrite keyword
dunder / “magic method”
double underscores before and after the word
Nicht bei Variablen machen!
a,b,c = 1,2,3
print(a)
print(b)
print(c)
expression vs statement in python
expression:
statement:
an entire line of code that performs a sort of action
+=
-=
*=
/=
augmented assignment operator
long_string = '''
WOW
O O
---
'''
print(long_string)
first_name = 'Marey'
last_name = 'Baden'
full_name = first_name + ‘ ' + last_name
print(full_name)
Marey Baden
type conversion
a = str(100)
b = int(a)
c = type(b)
escape sequence
weather = "it's "kind of" sunny"
weather = "it\'s \"kind of\" sunny"
backslash = whatever comes after this is a string
altgr + ß
\t
weather = "\t it\'s \"kind of\" sunny"
print(weather)
one tab
it's "kind of" sunny
\n
weather = "it\'s \"kind of\" sunny \nhope you have a nice day"
hope you have a nice day
f’
dont do
print ('hi ' + name + ', you are ' + age + ' years old')
formatted strings
do
print (f'hi {name}, you are {age} years old')
Submaps (bottom-up approach)
Manually curated and annotated molecular pathways, molecules and cell types for defined biological processes involved in acute inflammation and its resolution
created in CellDesigner
in order to maintain an organized and clean view, the submaps are the only part visible to the user when accessing the AIR web platform
Molecular interaction maps (MIMs) (top-down approach)
constructed around seed molecules involved in clinical inflammatory settings from various databases, e.g. DisGeNET, HPRD, and IntAct
Regulatory layers
Layers of micro RNA (miRNA), long non-coding RNA (lncRNA) and transcription factor (TF)
Interact to elements in the AIR
In order to maintain an organized and clean view when accessing the AIR web platform, …
… the submaps are the only part visible
The other interactions are stored externally and can be accessed by analysis tools (i.e. plugins)
Cytokines
They are signaling proteins that help control inflammation in the body
Some cytokines stimulate the immune system and others slow it down
Too many cytokines can lead to …
… excess inflammation and conditions like autoimmune diseases
homeostasis
this is the steady internal condition of optimal functioning for the organism and includes many variables, such as body temperatureand fluid balance, being kept within certain pre-set limits
Last changed9 days ago
